fungi

Fungi can be single celled or very complex multicellular organisms. General characteristic of fungus is eukaryotic, spore-bearing organism, no chlorophyll, reproduce sexually and asexually and absorbtive nutrition.They are found in just about any habitat but most live on the land, mainly in soil or on plant material rather than in sea or fresh water. A group called the decomposers grow in the soil or on dead plant matter where they play an important role in the cycling of carbon and other elements. This is the structure of fungus

Reproduction of fungi is sexual and asexual.

Asexual reproduction 1. Bud formation in yeasts In its simplest form asexual reproduction is by budding or binary fission. Enzymatic activity and turgor pressure the act to weaken and extrude the cell wall. New cell wall material is incorporated during this phase.

2. Fragmentation

Any mycelium that is fragmented or disrupted, provided that the fragment contains the equivalent of the peripheral growth zone, can grow into a new colony.

3. Sporulation

It is responsible for the production of large numbers of spores throughout the year. These asexual spores are formed on a phase of the fungal life cycle termed in some texts as the mitosporic, or anamorphic phase.

Sexual reproduction

To achieve sexual reproduction it is necessary to have two mating type haploid nuclei (n + n), or a diploid (2n) nucleus.

Zygomycota Common representatives: black bread molds Hyphae are haploid Reproduction relies mainly on asexual spore production

Ascomycota (sac fungi) Common representatives: yeasts, morels, and truffles Hyphae are haploid and dikaryoid Asexual reproduction relies on asexual spore production

Basidiomycota (sac fungi) Common representatives: mushrooms and shelf fungi Hyphae are haploid and dikaryoid Asexual reproduction relies on asexual spore production

Deuteromycota (fungi imperfecti)

• Members include Trichophyton (Athlete's foot), Penicillium (Penicillin), and Candida albicans 

There are three types of slime molds:

• Oomycota
• Myxomycota
• Acrasiomycota

A very small number of fungi cause diseases in animals. In humans these include skin diseases such as athletes’ foot, ringworm and thrush. And benefit of fungi is as agents of biodegradation, industrial fermentation process and important for agriculture, horticulture and forestry.

Archaea

This week we learn on archaea . Archaeans can be found in the most extreme environments on the planet which in cold environment, hot environment, high salinity and anaerobic environment.  They  live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot spring, or in extremely alkaline or acid waters. They have been found inside the digestive tracts of cows, termites, and marine life where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean.  

There are three main types of archaea: the crenarchaeota, which are characterized by their ability to tolerate extremes in temperature and acidity. The euryarchaeota, which include methane-producers and salt-lovers  and lastly is theaumarcheota. The unique features of archea is cell wall, membrane lipids , metabolism and genetics. Cell wall of bacteria contain s-layer that different from bacteria s-layer. Archaea membrane has their own features that differentiate it from bacteria that is more complex and less impermeable.

Among these three main types of archaea are some subtypes, which include:

Methanogens— archaeans that produce methane gas as a waste product of their "digestion," or process of making energy.

Halophiles— those archaeans that live in salty environments.

Thermophiles— the archaeans that live at extremely hot temperatures.

Psychrophiles— those that live at unusually cold temperatures.

that is what i can conclude from the notes of archaea . second class we have answer the group quiz on the procaryotic and archea

microbial systematic-bacteria

Today story… we divide into group to do a mind map on topic introduction to microbial systematic . our group doing on the outline of that topic . so for the outline we divide the work based on class which is archaea ,becteria ,virus ,fungi, protozoa and algae . we started with the group presentation on bacteria .  we need to know the differences between these group . next day , we learn on bacteria . we always culture the bacteria in the lab and all bacteria that we use lab is the bacteria that we can study. Archaea can change shape based on environment condition same goes to gram positive bacteria that doesn’t have cell wall and can change shape. The traits used to classify the bacteria is cell type , morphology, metabolism, reproduction, phage typing, nucleic acid profile and antibiotic resistance profile . we discuss on differences between the endospore and free spore . endospore form by the bacteria  while free spore are outside the cell . reproductive traits influence either light or oxygen. The bacteria E.coli , Salmonella , shigella can be observe difeerently because E.coli shown green sheen colour. Phatogen nonphototropic bacteria such as campylobacter and helicobacter,spirochetes and chlamydias . and nonphatogen is like pseudomonas,azobacter and rhizobium.  For phototrophic  we have oxygenic and nonoxygenic. 

topic 2 introduction to immunology

What means by immunology actually ? I concluded that immunology focuses on the human body's built-in defense system. In a healthy person, the immune system helps the body fight infection by rejecting foreign viruses and bacteria. The key primary lymphoid organs of the immune system are thymus and bone marrow, and secondary lymphatic tissues such as spleen, tonsils, lymph vessels, lymph nodes, adenoids, and skin. There are 3 lines of body defense system :

a)external physical barrier –skin,mucos membrane,normal microbiota

b)internal barrier-phagocytic cell, inflammation and fever

c)specific immune response-humoral response and humoral immune

therefore, we can differentiate between the non-specific annd specific immune response. their characteristic shown the differences between the non specific and non specific immune response which is non-specific immune response is natural immune system , without memory and non specific. While specific immune response is specificity,inducibility,memory,distinguish self and non-self. There are two type of non-specific immune response :

Internal innate immunity-2 line defense-physiological barrier,phagocytosis,inflammation

External innate immunity-1 line defense-skin, mucos membrane and normal microbiota

we need to know that an antigen need to have this features:

-high molecular weight

-complexity

-soluble

-foreigness

this is differences between the antigen and antibody

Humoral (Antibody-Mediated) Immunity

-Found in body fluids.

-Antibodies are made by plasma cells (activated B lymphocytes) in response to specific antigen.

Cell-Mediated Immunity

-T cells have antigen receptors but don’t make antibodies – lyse target cells directly.

-Cell-mediated reactions primarily respond against intracellular viruses, multicellular parasites, transplanted tissue and cancer cells.

after the lecture we all conclude all the mechanism of different types of immunity in this whiteboard

this mind map is very helpful in order to understand in systematic ways in immunology .After learn on this topic i know that Immune system keep us safe from infection and diseases. It helps us keep ourselves healthy.  Any disease that causing bacteria that enters our body is prevented from causing any damage to the body as the immune system deals with it. We know that every single breath that we inhale, every drop of water we drink or the every bite of food we eat, all contains germs and we are vulnerable to attack by germs. 

semester 2 Microbiologyll topic 1

For the second semester we already cover on topic microbial taxonomy and introduction to immunology . for topic microbial taxonomy we learn:

1)name microorganisms according to international rules and regulation
2)illustrate the methods to classify, identify and name the microorganism

CLASSIFICATION SYSTEM
Phenetic-Numerical taxonomy ,Dendogram
Phylogenetic-16S rRNA, Phylogenetic tree
Genotypic-other molecular methods

Phenetic classification is based on the mutual similarity of phenotypic characterstics. The are two methods in this classification which is simple matching coefficient and Jaccard coefficient.
Phylogenetic is compare organism on the basis of evolutionary. From this classification I will know how to determine phylogenetic classification.
For genotypic , I know that if we come from same species that related we have strong similarity.



TECHNIQUES/METHODS FOR CLASSIFICATION/IDENTIFICATION


Classical
· Morphological (staining, external structure, cell inclusion, cell grouping)
· Physiological and metabolic
· Biochemical
· Ecological
· Immunologic test
· Phage typing
· Antibiotic profiling


Molecular
· Amino acid sequencing
· Nucleic acid base composition (%GC by HPLC and Tm)
· Nucleic acid hybridization
· Nucleic acid sequencing
· Genomic fingerprint (MLSA, RFLP, ribotyping)
· Nucleic acid probe
· Plasmid fingerprinting


In nucleic acid base composition %GC , I know the steps to get the GC content by spectrophotometrically. I think this technique not very accurate because of same GC content but the arrangement differ are not relate . Nucleic acid hybridization also we need to remember the steps involve. This technique is strictly control to avoid self hybridize.

In bacteriophage typing , we need to remember the procedure to produce the plaque on agar plate. Antibiotic susceptibility test is use to determine the pattern of resistance and susceptibility to antibiotics by determination of MIC and MLC. By using this method , we can see the contract between the clear zone that show it susceptible to antibiotics where the bacteria cannot grow and resistance the bacterial growth.

From this lesson I know that it is not easy to give the bacterial names which we need to follow the rules and techniques in giving the name of bacterial. So I really appreciate and impress with the people that found every new bacterial for further studies. And there is a lot of technique and method for classification and identification of bacterial that we need to well planned the test to get the good identification .

19 December 2014

Today 19 December 2014, we learn on control of microbial growth. This is important term that we should remember:

• Sterilization: Removal of all microbial life

• Commercial sterilization: Killing C. Botulinum endospores

• Disinfection: Destruction/removal of pathogens

• Antisepsis: Destruction/removal of pathogens from living .

Tissue

• Degerming: Removal of microbes from a limited area

• Sanitization: Lower microbial counts on eating utensils

• Biocide/Germicide: Kills microbes

• Bacteriostasis: Inhibiting, not killing, microbes

In -cidal Agents,-cideis suffix indicating that agent kills and - static Agents,- static is suffix indicating that agent inhibits growth. Effectiveness of Antimicrobial Treatment is depends on number of microbes,Duration of exposure, Microbial characteristics, concentration or intensity of an antimicrobial agent, population composition, temperature, local environment.

There are three type of Physical Control Method which are Heat,Filtration,Radiation.

Moist Heat will destroys viruses, fungi, and bacteria. Steam Sterilization is carried out using an autoclave and effective against all types of microorganisms including spores. Dry heat sterilization kills by oxidation by Flaming,  Incineration, Hot-air sterilization and Less effective than moist heat sterilization. Low temperature inhibits microbial growth by Refrigeration, Deep freezing and Lyophilization. Filtration will reduces microbial population or sterilizes solutions of heat-sensitive materials by removing microorganisms. In radiation, we have uv radiation and gamma radiation.

There are three type of Chemical Control Agents which are Disinfection,Antisepsis and Sterilization. In Evaluating a disinfectant we Use-dilution test and  Disk-diffusion method. 

Lastly, we can determine the types of Disinfectants is Halogens – Iodine, Halogens – Chlorine, alcohol, heavy metal, Surface-active agents or surfactants,Chemical food preservatives, Aldehydes and sterilizing gases.

Then, we continue our lecture on the next topic which is antimicrobial chemotheraphy. I know that chemotherapeutic agents is a chemical agents used to treat disease. Penicillin discovered by Alexander Fleming to observe penicillin activity on contaminated plate. The general characteristic of antimicrobial drug are selective toxicity,therapeutic dose, toxic dose, therapeutic index, side effect, narrow-spectrum drugs, broad-spectrum drug,cidal agent and static agent,effect of an agent may very, and effectiveness expressed in two ways(MIC and MLC). Besides that, I can determine the level of antimicrobial activity which are dilution susceptibility test for MIC, disk diffusion tests, and the E-test MIC and diffusion. Antimicrobial drug is the inhibitor of cell wall synthesis, protein synthesis inhibitor, metabolic antagonists and nucleic acid synthesis inhibition. The in hibitors of cell wall synthesis are penicillins,cephalosporins, vancomycin and teicoplanin.

 Aminoglycoside antibiotics is large family which all contain a cyclohexane ring and amino sugars. Tetracyclines is all have a four-ring structure to which a variety of side chains are attached. Macrolides is used for patients allergic to penicillin. Chloramphenicol now is chemically synthesized. I also know that metabolic antagonist acts as antimetabolites and structural analogs. Nucleic acid synthesis inhibition will block DNA replication. Antifungal drugs has fewer effective agent. Antiviral drug development has been slow because it is difficult to specifically target viral replication. Anti-HIV drugs have reverse transcriptase inhibitors, protease inhibitors, fusion inhibitors and most successful are drug cocktails to curtail resistance. The antiprotozoal drug is the mechanism of drug action for antiprotozoal drug is not known. I also can identify factors influencing Antimicrobial Drugs which is:

• ability of drug to reach site of infection

• susceptibility of pathogen to drug

• ability of drug to reach concentrations

in body that exceed MIC of pathogen

Drug resistance will an increasing problem, microbes in abscesses or biofilms may be

growing slowly and resistance mutants arise spontaneously . since, today is our last class for this semester, I want to say thank you so much to dr.wan and pray us for success in exams later. I surely will remember all the sweet moment in this semester. thanks

Tuesday, 16 December

Tuesday, 16 December. We continue our lecture on isolation ,culturing , maintaining and preserving microbes. First, we need know the definition of aseptic technique. Aseptic technique refers to carrying out a procedure under controlled condition in a manner that will minimize the chance of contamination.

Culturing method have 2 basic technique which are liquid and qulture. Liquid can be reared in culture tubes in a liquid medium while qulture use plates where the liquid medium is solidified using agar and poured as a thin layer in the bottom of a culture dish.

Besides, we know how to get pure culture by using streak dilution plate methods.

this is how to obtain pure culture using pour plate method

there are 5 type of culture media which are chemically defined vs. complex media, liquid vs. semisolid media , selective media ,differential media and enrichment media.bacterial growth by budding, spores and fragmentation. Next, we learn on how to calculate number of generation and generation time .

This is the formula for the number of generation time and number of generation.

Generation time=60 min×hours)/ number of generation

Number of generation = Log number of cells (end) – log number of cells (beginning)

                                                                                   0.301

This is bacterial growth curve

Direct measurement of microbial growth , we use plate counts and filtration. Lastly, we can estimating the bacterial numbers by indirect methods using turbidity, periodic transfer of strains to fresh medium, incubate and store in the refrigerator,the short term storage and the long period storage.